Gene arrangement, phylogeny and divergence time estimation of mitogenomes in Thrips

Pakrashi, Avas; Kumar, Vikas; Stanford-Beale, David A. C.; Cameron, Stephen L.; Tyagi, Kaomud

doi:10.1007/s11033-022-07434-w

Cited by 8 publications

(12 citation statements)

References 61 publications

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“…The sequence of CR1 was identical to that of CR2 suggesting duplication of the control region as reported previously in thrips (Tyagi et al, 2020). Previously, four conserved Thrips Gene Blocks (TGBs) for suborder Terebrantia were proposed (Pakrashi et al, 2022), of which only one TGB‐2 ( cytb ‐ trnY ) was not found in the T. parvispinus mitogenome. Nevertheless, the shared gene boundaries ( cox2 ‐ trnG , atp6 ‐ trnQ , trnQ ‐ trnS2 , and rnL ‐ cox1 ) conserved for the genus Thrips were found as in previous studies (Pakrashi et al, 2022; Tyagi et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

“…The current comparative study found low nucleotide diversity, reversal of strand asymmetry, disparate codon usage patterns and strong purifying selection pressure in Tubulifera. Terebrantia are considered as more advanced and recently diverged lineages of order Thysanoptera as compared to Tubulifera (Pakrashi et al, 2022). Additionally, most of pest and vector thrips are terebrantians that are more active fliers than tubuliferans.…”

Section: Discussionmentioning

confidence: 99%

“…A previous study in phylogenetic analysis of 28 species of Thysanoptera (Pakrashi et al, 2022) showed the effectiveness of first and second codon positions only PCGs data set, with GBlocks removal (PCG12 + Gblocks) in resolving taxonomic boundaries in thrips. Here the phylogeny was constructed using 31 species (plus outgroup Alloeorhynchus bakeri Hemiptera) with the same data set strategy (PCG12 + Gblocks: 6014 bp).…”

Section: Methodsmentioning

confidence: 99%

“…previously carried out byPakrashi et al in 2022. The current study defines the phylogenetic position of three newly added species in order Thysanoptera; Bactrothrips quadrituberculatus, Psephenothrips eriobotryae, and Thrips parvispinus.…”

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confidence: 98%

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Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus

Pakrashi

Patidar

Singha

et al. 2023

Arch Insect Biochem Physiol

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Thrips parvispinus is a serious sucking pest on a number of economically important crops in the oriental region. It has gained importance recently for its drastic range extension distribution as an invasive pest. Here, the complete mitochondrial genome (15,067 bp) of Thrips parvispinus was sequenced and characterized. It possesses 37 genes and the putative noncoding region is duplicated. Comparative analyses of nucleotide diversity, skewness, codon usage bias, and selection pressure in mitochondrial protein‐coding genes of the available 31 thrips mitogenomes (24 Terebrantia + 7 Tubulifera) were performed. Phylogenetic analysis showed a sister relationship of T. parvispinus to the clade (T. florum + T. hawaiiensis). Phylogenetic analyses formed the monophyly of subfamilies Phlaeothripinae and Idolothripinae within the family Phlaeothripidae (Suborder Tubulifera). Low nucleotide diversity was indicative of reversal of strand asymmetry in the Tubulifera. Neutrality analysis showed that directional mutation plays a major role in shaping codon usage bias in both suborders. Principal component analysis indicated distinct codon usage patterns in each suborder. Our data suggested weaker selection constrains on Terebrantia than in the Tubulifera. More tubuliferan mitogenomes are required to resolve previous classification hypotheses and elucidate genome evolution in these two suborders.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 98%

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Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus

Pakrashi

Patidar

Singha

et al. 2023

Arch Insect Biochem Physiol

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“…However, recently, some authors proposed that the presence of multiple CRs and gene rearrangement is not causal (Tyagi et al, 2020). The thrip phylogeny is intensively studied, and classification systems based on mitogenomes were proposed (Liu et al, 2022;Pakrashi et al, 2022Pakrashi et al, , 2023Tyagi et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta)

Meng,

Wang,

Pang

et al. 2024

Arch Insect Biochem Physiol

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The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age‐related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple‐CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.

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Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera)

Ghosh,

Tyagi,

Dubey

et al. 2024

Funct Integr Genomics

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Gene arrangement, phylogeny and divergence time estimation of mitogenomes in Thrips

Cited by 8 publications

References 61 publications

Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus

Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus

Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta)

Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera)

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